Global change differentially modulates physiological plasticity of tropical reef-building corals
Last run on 03 February 2022
Principal component analyses
Methods:
Principal component analysis (PCA) (function prcomp) of scaled and centered physiological parameters (host carbohydrate, host lipid, host protein, algal symbiont chlorophyll a, algal symbiont cell density, calcification rate as previously for the same samples in Bove et al (2019)) were employed to assess the relationship between physiological parameters and treatment conditions for each coral species. Main effects (temperature, pCO2, reef environment) were evaluated with PERMANOVA using the adonis2 function (vegan package; version 2.5.7 (Oksanen et al., 2020)). No interactions between main effects were identified as significant, so interaction terms were dropped from each model resulting in fully additive models.
Siderastrea siderea
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 1500
##
## adonis2(formula = sid_pca_df ~ fpco2 + ftemp + reef, data = s_df, permutations = bootnum, method = "eu", by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## fpco2 3 59423 0.20282 7.9334 0.0006662 ***
## ftemp 1 9320 0.03181 3.7329 0.0546302 .
## reef 1 24705 0.08432 9.8948 0.0013324 **
## Residual 80 199740 0.68174
## Total 85 292988 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Pseudodiploria strigosa
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 1500
##
## adonis2(formula = dip_pca_df ~ reef + ftemp + fpco2, data = p_df, permutations = bootnum, method = "eu", by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## reef 1 101796 0.09008 14.8653 0.0006662 ***
## ftemp 1 519372 0.45958 75.8438 0.0006662 ***
## fpco2 3 30444 0.02694 1.4819 0.2225183
## Residual 71 486202 0.43023
## Total 76 1130099 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Porites astreoides
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 1500
##
## adonis2(formula = por_pca_df ~ reef + ftemp + fpco2, data = a_df, permutations = bootnum, method = "eu", by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## reef 1 724 0.00512 0.5264 0.4856762
## ftemp 1 27051 0.19129 19.6601 0.0013324 **
## fpco2 3 30537 0.21594 7.3978 0.0006662 ***
## Residual 62 85309 0.60325
## Total 67 141417 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Figure 1
Figure 1. Principal component analysis (PCA) of all coral holobiont physiological parameters for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93 days of exposure to different temperature and pCO2 treatments. PCAs in the top row are depicted by temperature treatment for each species (28\(^\circ\)C blue; 31\(^\circ\)C red) and the bottom row of PCAs are depicted by pCO2 for each species (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters (rate = calcification rate; den = symbiont density; chla = chlorophyll a; pro = protein; carb = carbohydrate; lipid = lipid; sum/red = color intensity) and ellipses represent 95% confidence based on multivariate t-distributions.
Figure 4
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 1500
##
## adonis2(formula = all_pca_df ~ fpco2 + ftemp + reef + species + ftemp:species + fpco2:species + reef:species, data = all_df, permutations = bootnum, method = "eu")
## Df SumOfSqs R2 F Pr(>F)
## fpco2 3 149393 0.03848 8.2405 0.0006662 ***
## ftemp 1 17313 0.00446 2.8650 0.0966023 .
## reef 1 58058 0.01496 9.6075 0.0013324 **
## species 2 1642613 0.42313 135.9102 0.0006662 ***
## ftemp:species 2 553351 0.14254 45.7844 0.0006662 ***
## fpco2:species 6 90865 0.02341 2.5061 0.0206529 *
## reef:species 2 77259 0.01990 6.3924 0.0026649 **
## Residual 214 1293204 0.33312
## Total 231 3882055 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Figure 4. Principal component analysis (PCA) comparing the coral holobiont of all three species at the end of the experiment depicted by (A) species, (B) pCO2 treatment, and (C) temperature treatment. Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Results
Principal component analysis
Two principal components (PCs) explained approximately 66% of the variance in physiological responses of the S. siderea holobiont to ocean acidification and warming treatments (Figure 1A). PC1 was driven by differences in algal symbiont physiology (chlorophyll a, cell density), while PC2 represented an inverse relationship between host energy reserves (lipid, protein, carbohydrate) and calcification rates and color intensities. Overall, lower pCO2 and temperature resulted in higher S. siderea holobiont physiology (Figure 1A). Treatment pCO2 predominantly drove S. siderea physiological responses (p = 7e-04; Table S4), while temperature and reef environment did not explain as much variation in physiological responses (p = 0.05 and p = 0.001, respectively; Table S4; Figure S3A).
For P. strigosa, 74% of the variance in the holobiont responses to treatments was explained by two PCs (Figure 1B). PC1 explained most of the variation of physiological parameters with the exception of host lipid content, which was represented in PC2. Holobiont physiology of P. strigosa was reduced under warming (p = 7e-04; Table S4) and in offshore samples (p = 7e-04; Table S4; Figure S3B), however, pCO2 did not clearly impact holobiont physiology (Figure 1B; p = 0.2; Table S4).
For P. astreoides, the first two PCs explained about 59% of the total variance in holobiont response to treatment (Figure 1C). Samples separated most clearly along PC1 driven primarily by calcification rate and algal symbiont density, while PC2 exhibited an inverse relationship between host total carbohydrate and color intensity. Overall, lower pCO2 drove higher P. astreoides holobiont physiology, while elevated temperature resulted in greater holobiont physiology (Figure 1C). Temperature (p = 0.001; Table S4) and pCO2 (p = 7e-04; Table S4) clearly altered P. astreoides holobiont physiology, while reef environment was not significant (p = 0.5; Table S4; Figure S3C).
Species differences in coral holobiont physiology
The first two PCs of the combined holobiont physiology explained about 62% of the total variance across samples (Figure 4). In general, fragments of S. siderea contained higher chlorophyll a content, host carbohydrate, and host lipid content, while P. strigosa fragments typically had greater host protein content accompanied by higher calcification rates, and fragments of P. astreoides were differentiated by their high symbiont densities (Figure 4A; Table S7). Despite being different coral species, coral holobiont physiology exhibited similar physiological responses to pCO2 and temperature treatments (Figure 4B, 4C; Table S7). As pCO2 or temperature increased, coral holobiont physiology was more constrained and exhibited convergent physiological responses under stress. Furthermore, corals from the inshore reef environment exhibited more constrained physiology than their offshore counterparts (Figure S9; Table S7).
Correlation assessments
Methods:
Correlations of all physiological parameters were assessed to determine the relationships between parameters within each species. The Pearson correlation coefficient (R2) of each comparison was calculated using the corrgram package (version 1.14 (Wright, 2018)) and the significance was calculated using the cor.test function. These relationships were then visualized through simple scatterplots.
Figure 2
Figure 2. Coral holobiont physiological parameter scatter plots (top) and correlation matrices (bottom) for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides showing pairwise comparisons of within each species. Scatter plots of each pairwise combination of physiological parameters are displayed on the top with temperature treatment depicted by shape (28\(^\circ\)C closed points; 31\(^\circ\)C open points) and pCO2 treatment depicted by color (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange). Strengths of the correlations (R2 via Pearson correlation coefficients) between each pairwise combination of physiological parameters are indicated by darker shades of blue on the bottom with significance depicted by asterisks according to significance level (* p < 0.05; ** p < 0.01; *** p < 0.001). R2 and significance levels correspond to the scatter plot at the intersection between two physiological parameters.
Results
Correlations of physiological parameters
Coral holobiont physiological parameters were generally positively correlated with one another within each of the three species. Correlations between S. siderea holobiont physiological parameters identified 15 significant relationships out of all 21 possible comparisons (Figure 2A). Of those significant correlations, six resulted in a Pearson’s correlation coefficient (R2) equal to or greater than 0.5, with the strongest relationship identified between symbiont density and chlorophyll a (R2 = 0.72).
All pairwise physiological parameters were significantly correlated with one another in P. strigosa and, of those, 15 correlations exhibit moderate (R2 > 0.50) positive relationships (Figure 2B). Notably, the two strongest correlations were host carbohydrate vs. host protein (R2 = 0.70) and host carbohydrate vs. chlorophyll a (R2 = 0.76).
Compared to both S. siderea and P. strigosa, fewer physiological traits were significantly (p < 0.05) correlated with one another in P. astreoides (12 significant out of 21 total comparisons; Figure 2C). Of the significant correlations, only two pairwise comparisons resulted in a Pearson’s correlation coefficient greater than 0.5: chlorophyll a vs. color intensity (R2 = 0.57) and host carbohydrate vs. host protein (R2 = 0.68).
Plasticity analyses
Methods:
Physiological plasticity of each experimental fragment was calculated for each species using all seven PCs calculated above as the distance between an experimental fragment and the control (420 \(\mu\)atm; 28\(^\circ\)C) fragment from that same colony. The effects of treatment (pCO2 and temperature) and natal reef environment on calculated distances were assessed using generalized linear mixed effects models (function lmer) with a Gamma distribution and log-link and a random effect for colony. The best-fit model was selected as the model with the lowest AIC for each species (Table S3). Natal reef environment was only a significant predictor of plasticity in S. siderea so samples were pooled across reef environments for both P. strigosa and P. astreoides. Parametric bootstraps were performed to model mean response and 95% confidence intervals with 1500 iterations and significant effects were identified as non-overlapping confidence intervals. Marginal and conditional R2 values were calculated using the r2_nakagawa function in the rcompanion package (version 2.4.1 (Mangiafico, 2021)). All figures and statistical analyses were carried out in R version 3.6.3 (R Core Team, 2018) and the accompanying data and code can be freely accessed on GitHub (github.com/seabove7/Bove_CoralPhysiology) and Zenodo (DOI here when close to finished).
Siderastrea siderea
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: Gamma ( log )
## Formula: dist ~ reef * fpco2 + ftemp + (1 | colony) + (1 | tank)
## Data: sid_dist
##
## AIC BIC logLik deviance df.resid
## 218.4 245.4 -97.2 194.4 58
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.92132 -0.66729 -0.00254 0.42115 2.51068
##
## Random effects:
## Groups Name Variance Std.Dev.
## tank (Intercept) 0.01357 0.1165
## colony (Intercept) 0.03209 0.1791
## Residual 0.08867 0.2978
## Number of obs: 70, groups: tank, 21; colony, 11
##
## Fixed effects:
## Estimate Std. Error t value Pr(>|z|)
## (Intercept) 1.050385 0.005617 187.007 <2e-16 ***
## reefN 0.009728 0.005650 1.722 0.0851 .
## fpco2420 0.378300 0.005650 66.954 <2e-16 ***
## fpco2680 0.222648 0.005663 39.316 <2e-16 ***
## fpco23290 0.443555 0.005632 78.751 <2e-16 ***
## ftemp31 0.001769 0.005625 0.314 0.7531
## reefN:fpco2420 -0.770729 0.005634 -136.809 <2e-16 ***
## reefN:fpco2680 -0.445519 0.005616 -79.326 <2e-16 ***
## reefN:fpco23290 -0.329693 0.005637 -58.483 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) reefN fp2420 fp2680 f23290 ftmp31 rN:242 rN:268
## reefN -0.003
## fpco2420 0.001 -0.002
## fpco2680 -0.005 0.001 -0.001
## fpco23290 0.003 0.001 -0.001 0.005
## ftemp31 -0.005 -0.002 0.000 -0.005 0.001
## rfN:fpc2420 0.001 0.001 -0.002 0.005 -0.001 0.001
## rfN:fpc2680 -0.005 -0.002 0.002 0.003 0.005 -0.004 0.005
## rfN:fp23290 -0.001 -0.002 0.002 0.001 -0.001 0.000 0.001 0.000
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.0126567 (tol = 0.002, component 1)## # R2 for Mixed Models
##
## Conditional R2: 0.542
## Marginal R2: 0.307
Pseudodiploria strigosa
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: Gamma ( log )
## Formula: dist ~ fpco2 + ftemp + (1 | colony)
## Data: dip_dist
##
## AIC BIC logLik deviance df.resid
## 97.5 104.8 -42.7 85.5 19
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.70079 -0.72697 0.05779 0.77668 2.01138
##
## Random effects:
## Groups Name Variance Std.Dev.
## colony (Intercept) 0.007898 0.08887
## Residual 0.137879 0.37132
## Number of obs: 25, groups: colony, 5
##
## Fixed effects:
## Estimate Std. Error t value Pr(>|z|)
## (Intercept) 1.27912 0.14767 8.662 <2e-16 ***
## fpco2680 -0.33844 0.19338 -1.750 0.0801 .
## fpco23290 -0.05892 0.18739 -0.314 0.7532
## ftemp31 0.22671 0.17289 1.311 0.1898
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fp2680 f23290
## fpco2680 -0.579
## fpco23290 -0.578 0.484
## ftemp31 -0.334 0.066 0.012## # R2 for Mixed Models
##
## Conditional R2: 0.232
## Marginal R2: 0.188
Porites astreoides
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: Gamma ( log )
## Formula: dist ~ fpco2 + ftemp + (1 | colony) + (1 | tank)
## Data: por_dist
##
## AIC BIC logLik deviance df.resid
## 142.4 158.3 -63.2 126.4 46
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.6543 -0.5670 -0.1035 0.5470 2.2029
##
## Random effects:
## Groups Name Variance Std.Dev.
## tank (Intercept) 0.001233 0.03512
## colony (Intercept) 0.037406 0.19341
## Residual 0.056156 0.23697
## Number of obs: 54, groups: tank, 21; colony, 11
##
## Fixed effects:
## Estimate Std. Error t value Pr(>|z|)
## (Intercept) 1.03344 0.12525 8.251 < 2e-16 ***
## fpco2420 -0.04516 0.11478 -0.393 0.693975
## fpco2680 0.03277 0.07852 0.417 0.676454
## fpco23290 0.12410 0.08225 1.509 0.131342
## ftemp31 0.26204 0.06856 3.822 0.000132 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fp2420 fp2680 f23290
## fpco2420 -0.153
## fpco2680 -0.318 0.380
## fpco23290 -0.353 0.306 0.526
## ftemp31 -0.166 -0.379 -0.073 0.068## # R2 for Mixed Models
##
## Conditional R2: 0.493
## Marginal R2: 0.145
Figure 3
Figure 3. Holobiont physiological plasticity of (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93-day exposure to experimental treatments. Higher values represent greater plasticity in coral holobiont samples. Natal reef environment is depicted along the x axis for S. siderea, however, P. strigosa and and P. astreoides samples were pooled by reef environment. pCO2 treatment is depicted by color and shape (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange) and temperature is represented as either closed (28 \(^\circ\)C) or open (31 \(^\circ\)C) symbols. The current day at 28 °C treatment is not depicted here since plasticity is represented as the distance from this treatment (420 μatm at 28 °C). Symbols and bars indicate modeled means and 95% confidence intervals.
Results
Coral holobiont physiological plasticity
Physiological plasticity of offshore S. siderea fragments exhibited a positive linear trend with increasing pCO2 while the inshore fragments appear to respond in a parabolic pattern to pCO2, with the lowest calculated distances occurring at 420 \(\mu\)atm, 31\(^\circ\)C and 680 \(\mu\)atm, 28\(^\circ\)C (Figure 3A). Further, offshore S. siderea fragments exhibited higher plasticity in the extreme pCO2 treatment than in inshore fragments reared in the pre-industrial, current-day, and extreme pCO2 treatments, regardless of temperature (Figure 3A; Table S5).
Plasticity of P. strigosa and P. astreoides was not clearly different between colonies based on natal reef environments (see Table S3). No clear differences in physiological plasticity in response to treatment were identified in P.strigosa (Figure 3B; Table S5), however, this is likely due to reduced sample sizes in this analysis as a result of only five colonies (Noffshore = 3, Ninshore = 2) present in the control treatment for distance calculations.
Elevated temperatures generally resulted in higher plasticity of P. astreoides compared to control temperatures (Figure 3C; Table S5), however, this trend was not clearly different within each pCO2 treatment. Physiological plasticity of P. astreoides was significantly lower in both the pre-industrial and end-of-century pCO2 treatments at control temperatures than that measured in the extreme pCO2 treatment combined with the elevated temperature.
Supplemental Figures
Figure S1
Figure S1. Diagram showing allocation of coral fragments for a single species throughout experimental tank array. Color represent a different colony and shape represents reef environment. Four colonies (two from each reef environment) are reared within each tank (grey box), with three tanks comprising a treatment (white box). This is repeated for each pCO2 treatment at both temperatures. This same experimental design was used for all species. Figure taken from Bove et al. 2019.
Figure S2
Figure S2. Calculated and measured seawater parameters over the entire experimental period.
Figure S3
Figure S3. Principal component analysis (PCA) of all coral physiological parameters for S. siderea, P. strigosa, and P. astreoides depicted by natal reef environment (A-C; offshore green, inshore yellow) and the combination of pCO2 and temperature treatment (D-F). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Figure S4
Figure S4. Principal component analysis (PCA) of S. siderea coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Figure S5
Figure S5. Principal component analysis (PCA) of P. strigosa coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Figure S6
Figure S6. Principal component analysis (PCA) of P. asteroides coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Figure S7
Figure S7. Coral host vs. algal symbiont physiological plasticity of (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93-day exposure to experimental treatments. Higher values represent greater plasticity in coral holobiont samples. pCO2 treatment is depicted by color and shape (pre industrial [300 μatm], light purple; current day [420 μatm], dark purple; end-of-century [680 μatm], light orange; extreme [3290 μatm], dark orange) and temperature is represented as either closed (28 °C) or open (31 °C) symbols. Symbols and bars indicate modeled means and 95% confidence intervals.
Figure S8
Figure S8. Mean (\(\pm\)SE) physiological parameter (each row) measured for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides at the completion of the 93-day experimental period. pCO2 treatment is represented along the x axis and the temperature is depicted by color (28\(^\circ\)C blue; 31\(^\circ\)C red).
Figure S9
Figure S9. Coral color changes over the experimental period. Representative images of fragments of (A) P. astreoides, (B) S. siderea, and (C) P. strigosa from the same colonies demonstrating change in coral color over time in either control (420 μatm; 28 °C) or warming (420 μatm; 31 °C) treatments from the start of the experiment (T0) to the end (T90).
Figure S10
Figure S10. Principal component analysis (PCA) comparing the physiology of all three species at the end of the experiment depicted by (A) reef environment and (B) combined pCO2 and temperature treatment. Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.
Supplemental Tables
Table S1
Table S1. Number samples per species per treatment assessed in physiological and plasticity analyses. Note that plasticity sample sizes are smaller due to comparison within colony resulting in reduced samples when a control fragment was not present.
| Treatment | Offshore | Inshore | Offshore | Inshore | |
|---|---|---|---|---|---|
| Porites astreoides | |||||
| current day (uatm) | 28C | 6 | 6 | ||
| current day (uatm) | 31C | 2 | 4 | 2 | 4 |
| end-of-century (uatm) | 28C | 6 | 6 | 5 | 6 |
| end-of-century (uatm) | 31C | 0 | 4 | 0 | 4 |
| extreme (uatm) | 28C | 5 | 5 | 5 | 5 |
| extreme (uatm) | 31C | 3 | 5 | 3 | 5 |
| pre industrial (uatm) | 28C | 6 | 5 | 5 | 5 |
| pre industrial (uatm) | 31C | 3 | 3 | 2 | 3 |
| Pseudodiploria strigosa | |||||
| current day (uatm) | 28C | 3 | 2 | ||
| current day (uatm) | 31C | 3 | 2 | 0 | 0 |
| end-of-century (uatm) | 28C | 9 | 6 | 4 | 2 |
| end-of-century (uatm) | 31C | 5 | 3 | 2 | 1 |
| extreme (uatm) | 28C | 8 | 6 | 3 | 2 |
| extreme (uatm) | 31C | 3 | 2 | 2 | 0 |
| pre industrial (uatm) | 28C | 10 | 6 | 4 | 2 |
| pre industrial (uatm) | 31C | 5 | 4 | 2 | 1 |
| Siderastrea Siderea | |||||
| current day (uatm) | 28C | 6 | 5 | ||
| current day (uatm) | 31C | 5 | 6 | 5 | 5 |
| end-of-century (uatm) | 28C | 6 | 6 | 6 | 5 |
| end-of-century (uatm) | 31C | 6 | 6 | 6 | 5 |
| extreme (uatm) | 28C | 7 | 5 | 7 | 4 |
| extreme (uatm) | 31C | 6 | 5 | 6 | 4 |
| pre industrial (uatm) | 28C | 6 | 4 | 6 | 4 |
| pre industrial (uatm) | 31C | 3 | 4 | 3 | 4 |
Table S2
Table S2. PERMANOVA model assessment for best-fit model selection of PCAs per species. Akaike information criterion (AIC) was used to select the best-fit model per species. For all species, the fully additive model was the best-fit model (temperature + pCO2 + reef).
| Species | Full interactive model AIC | Best fit (additive) model AIC |
|---|---|---|
| S. siderea | 692.3 | 678.5 |
| P. strigosa | 696.9 | 685.8 |
| P. astreoides | 500.5 | 497.1 |
Table S3
Table S3. Model performance comparisons of generalized linear mixed effects models (GLMM) for plasticity assessments to select the best-fit model per species using the package performance (version 0.7.3). Akaike information criterion (AIC) was used to select the best-fit model per species. The models highlighted in grey were used for bootstrapping estimates and 95% confidence intervals.
| Model formula | AIC | Conditional R2 | Marginal R2 |
|---|---|---|---|
| Siderastrea Siderea | |||
| reef environment * pCO2 * temperature + (1 | colony) | 223.2 | 0.545 | 0.366 |
| reef environment * pCO2 + temperature + (1 | colony) | 218.8 | 0.506 | 0.322 |
| reef environment * pCO2 + temperature + (1 | colony) + (1 | tank) | 218.4 | 0.542 | 0.307 |
| reef environment + pCO2 * temperature + (1 | colony) | 225.6 | 0.442 | 0.253 |
| reef environment + pCO2 + temperature + (1 | colony) | 221.6 | 0.442 | 0.254 |
| reef environment * (pCO2 + temperature) + (1 | colony) | 220.1 | 0.511 | 0.329 |
| pCO2 + temperature + (1 | colony) | 222.1 | 0.370 | 0.088 |
| Pseudodiploria strigosa | |||
| reef environment * pCO2 * temperature + (1 | colony) | 110.7 | 0.427 | 0.347 |
| reef environment * pCO2 + temperature + (1 | colony) | 106.0 | 0.341 | 0.292 |
| reef environment + pCO2 * temperature + (1 | colony) | 106.9 | 0.313 | 0.271 |
| pCO2 + temperature + (1 | colony) | 102.8 | 0.268 | 0.224 |
| Porites astreoides | |||
| reef environment * pCO2 * temperature + (1 | colony) | 153.1 | 0.527 | 0.199 |
| reef environment * pCO2 + temperature + (1 | colony) | 145.9 | 0.521 | 0.195 |
| reef environment + pCO2 * temperature + (1 | colony) | 146.2 | 0.500 | 0.174 |
| reef environment + pCO2 + temperature + (1 | colony) | 142.3 | 0.499 | 0.174 |
| reef environment * (pCO2 + temperature) + (1 | colony) | 147.9 | 0.522 | 0.195 |
| pCO2 + temperature + (1 | colony) | 140.4 | 0.485 | 0.147 |
| pCO2 + temperature + (1 | colony) + (1 | tank) | 142.4 | 0.493 | 0.145 |
Table S4
Table S4. PERMANOVA model output from each species using the adonis2 function with 1500 iterations.| Df | Sum of Squares | R2 | F | P-value | |
|---|---|---|---|---|---|
| Siderastrea Siderea | |||||
| pCO2 | 3 | 59423 | 0.203 | 7.93 | 0.00067 |
| temperature | 1 | 9320 | 0.032 | 3.73 | 0.05463 |
| reef environment | 1 | 24705 | 0.084 | 9.89 | 0.00133 |
| Residual | 80 | 199740 | 0.682 | ||
| Total | 85 | 292988 | 1.000 | ||
| Pseudodiploria strigosa | |||||
| reef environment | 1 | 101796 | 0.090 | 14.87 | 0.00067 |
| temperature | 1 | 519372 | 0.460 | 75.84 | 0.00067 |
| pCO2 | 3 | 30444 | 0.027 | 1.48 | 0.22252 |
| Residual | 71 | 486202 | 0.430 | ||
| Total | 76 | 1130099 | 1.000 | ||
| Porites astreoides | |||||
| reef environment | 1 | 724 | 0.005 | 0.53 | 0.48568 |
| temperature | 1 | 27051 | 0.191 | 19.66 | 0.00133 |
| pCO2 | 3 | 30537 | 0.216 | 7.40 | 0.00067 |
| Residual | 62 | 85309 | 0.603 | ||
| Total | 67 | 141417 | 1.000 | ||
Table S5
Table S5. GLMM output from plasticity assessments for each species. The intercept of each model was set as 300 \(\mu\)atm, 28\(^\circ\)C, and inshore reef environment.| Estimate | Standard error | Statistic | P-value | |
|---|---|---|---|---|
| Siderastrea Siderea | ||||
| (Intercept) | 1.050 | 0.006 | 187.01 | 0.000 |
| reef environment (offshore) | 0.010 | 0.006 | 1.72 | 0.085 |
| pCO2-current | 0.378 | 0.006 | 66.95 | 0.000 |
| pCO2-EOC | 0.223 | 0.006 | 39.32 | 0.000 |
| pCO2-extreme | 0.444 | 0.006 | 78.75 | 0.000 |
| temperature (31C) | 0.002 | 0.006 | 0.31 | 0.753 |
| reef environment (offshore):pCO2-current | -0.771 | 0.006 | -136.81 | 0.000 |
| reef environment (offshore):pCO2-EOC | -0.446 | 0.006 | -79.33 | 0.000 |
| reef environment (offshore):pCO2-extreme | -0.330 | 0.006 | -58.48 | 0.000 |
| Conditional R2 | 0.542 | |||
| Marginal R2 | 0.307 | |||
| Pseudodiploria strigosa | ||||
| (Intercept) | 1.279 | 0.148 | 8.66 | 0.000 |
| pCO2-EOC | -0.338 | 0.193 | -1.75 | 0.080 |
| pCO2-extreme | -0.059 | 0.187 | -0.31 | 0.753 |
| temperature (31C) | 0.227 | 0.173 | 1.31 | 0.190 |
| Conditional R2 | 0.232 | |||
| Marginal R2 | 0.188 | |||
| Porites astreoides | ||||
| (Intercept) | 1.033 | 0.125 | 8.25 | 0.000 |
| pCO2-current | -0.045 | 0.115 | -0.39 | 0.694 |
| pCO2-EOC | 0.033 | 0.079 | 0.42 | 0.676 |
| pCO2-extreme | 0.124 | 0.082 | 1.51 | 0.131 |
| temperature (31C) | 0.262 | 0.069 | 3.82 | 0.000 |
| Conditional R2 | 0.493 | |||
| Marginal R2 | 0.145 | |||
Table S6
Table S6. PERMANOVA model output across species using the adonis2 function with 1500 iterations.| Df | Sum of Squares | R2 | F | P-value | |
|---|---|---|---|---|---|
| pCO2 | 3 | 149393 | 0.038 | 8.24 | 0.00067 |
| temperature | 1 | 17313 | 0.004 | 2.87 | 0.09660 |
| reef environment | 1 | 58058 | 0.015 | 9.61 | 0.00133 |
| species | 2 | 1642613 | 0.423 | 135.91 | 0.00067 |
| temperature:species | 2 | 553351 | 0.143 | 45.78 | 0.00067 |
| pCO2:species | 6 | 90865 | 0.023 | 2.51 | 0.02065 |
| reef environment:species | 2 | 77259 | 0.020 | 6.39 | 0.00266 |
| Residual | 214 | 1293204 | 0.333 | ||
| Total | 231 | 3882055 | 1.000 |
Table S7
Table S7. PERMANOVA model output of coral host or algal symbiont physiology per species using the adonis2 function with 1500 iterations depicted in Figures S2-S4.| Df | Sum of Squares | R2 | F | P-value | Df | Sum of Squares | R2 | F | P-value | |
|---|---|---|---|---|---|---|---|---|---|---|
| Siderastrea Siderea | ||||||||||
| pCO2 | 3 | 1 | 0.019 | 0.55 | 0.77615 | 3 | 61056 | 0.208 | 8.15 | 0.00067 |
| temperature | 1 | 3 | 0.075 | 6.65 | 0.00200 | 1 | 7468 | 0.025 | 2.99 | 0.09061 |
| reef environment | 1 | 0 | 0.006 | 0.52 | 0.58894 | 1 | 24705 | 0.084 | 9.90 | 0.00266 |
| Residual | 80 | 30 | 0.901 | 80 | 199684 | 0.682 | ||||
| Total | 85 | 34 | 1.000 | 85 | 292913 | 1.000 | ||||
| Pseudodiploria strigosa | ||||||||||
| pCO2 | 3 | 1 | 0.041 | 1.23 | 0.26382 | 3 | 26899 | 0.024 | 1.31 | 0.27848 |
| temperature | 1 | 3 | 0.147 | 13.12 | 0.00067 | 1 | 515173 | 0.456 | 75.24 | 0.00067 |
| reef environment | 1 | 0 | 0.020 | 1.75 | 0.17255 | 1 | 101793 | 0.090 | 14.87 | 0.00200 |
| Residual | 71 | 14 | 0.793 | 71 | 486140 | 0.430 | ||||
| Total | 76 | 18 | 1.000 | 76 | 1130005 | 1.000 | ||||
| Porites astreoides | ||||||||||
| pCO2 | 3 | 2 | 0.136 | 3.48 | 0.01666 | 3 | 29037 | 0.205 | 7.04 | 0.00067 |
| temperature | 1 | 0 | 0.036 | 2.76 | 0.10193 | 1 | 26338 | 0.186 | 19.15 | 0.00067 |
| reef environment | 1 | 0 | 0.021 | 1.64 | 0.19920 | 1 | 724 | 0.005 | 0.53 | 0.48168 |
| Residual | 62 | 10 | 0.807 | 62 | 85288 | 0.603 | ||||
| Total | 67 | 13 | 1.000 | 67 | 141387 | 1.000 | ||||
Table S8
Table S8. Model performance comparisons of generalized linear mixed effects models (GLMM) for plasticity assessments to select the best-fit model comparing host and symbiont using the package performance (version 0.7.3). Akaike information criterion (AIC) was used to select the best-fit model. The models highlighted in grey were used for bootstrapping estimates and 95% confidence intervals.| Model formula | AIC | Conditional R2 | Marginal R2 |
|---|---|---|---|
| species * part * reef environment * pCO2 * temperature + (1 | colony) | 923.1 | 0.430 | 0.318 |
| species * part * reef environment * pCO2 + temperature + (1 | colony) | 904.6 | 0.338 | 0.225 |
| species * part * reef environment + pCO2 * temperature + (1 | colony) | 890.2 | 0.222 | 0.113 |
| species * reef environment + part + pCO2 + temperature + (1 | colony) | 881.2 | 0.205 | 0.095 |
| species * part * reef environment * (pCO2 + temperature) + (1 | colony) | 902.1 | 0.391 | 0.279 |
| species * part * pCO2 + temperature + (1 | colony) | 890.2 | 0.235 | 0.093 |
| reef environment * species * part * (pCO2 + temperature) + (1 | colony) | 902.1 | 0.391 | 0.279 |
| reef environment * species * part * (pCO2 + temperature) + (1 | colony) | 902.1 | 0.391 | 0.279 |
| species * part * (pCO2 + temperature) + (1 | colony) | 882.0 | 0.280 | 0.139 |
| species * part * (pCO2 + temperature) + reef environment + (1 | colony) | 883.5 | 0.282 | 0.144 |
| species * part * (pCO2 + temperature + reef environment) + (1 | colony) | 883.9 | 0.323 | 0.212 |
Table S9
Table S9. GLMM output from plasticity assessments for coral host vs. algal symbiont for each species. The intercept of each model was set as coral host, S. siderea, 300 \(\mu\)atm, and 28\(^\circ\)C.| Estimate | Standard error | Statistic | P-value | |
|---|---|---|---|---|
| (Intercept) | 0.800 | 0.172 | 4.66 | 0.000 |
| PSTR | 0.199 | 0.290 | 0.69 | 0.492 |
| PAST | -0.357 | 0.244 | -1.46 | 0.143 |
| symbionts | -0.515 | 0.185 | -2.78 | 0.005 |
| pCO2-current | 0.234 | 0.214 | 1.10 | 0.273 |
| pCO2-EOC | 0.005 | 0.164 | 0.03 | 0.974 |
| pCO2-extreme | -0.021 | 0.161 | -0.13 | 0.895 |
| temperature (31C) | -0.252 | 0.128 | -1.96 | 0.050 |
| PSTR:symbionts | 0.223 | 0.308 | 0.72 | 0.470 |
| PAST:symbionts | 0.685 | 0.270 | 2.53 | 0.011 |
| PSTR:pCO2-current | -0.088 | 0.592 | -0.15 | 0.882 |
| PAST:pCO2-current | -0.568 | 0.339 | -1.68 | 0.094 |
| PSTR:pCO2-EOC | -0.450 | 0.298 | -1.51 | 0.131 |
| PAST:pCO2-EOC | 0.051 | 0.240 | 0.21 | 0.833 |
| PSTR:pCO2-extreme | -0.154 | 0.288 | -0.53 | 0.593 |
| PAST:pCO2-extreme | 0.236 | 0.245 | 0.96 | 0.335 |
| PSTR:temperature (31C) | 0.072 | 0.250 | 0.29 | 0.774 |
| PAST:temperature (31C) | 0.608 | 0.200 | 3.04 | 0.002 |
| symbionts:pCO2-current | -0.299 | 0.298 | -1.00 | 0.316 |
| symbionts:pCO2-EOC | 0.134 | 0.227 | 0.59 | 0.555 |
| symbionts:pCO2-extreme | 0.564 | 0.226 | 2.50 | 0.013 |
| symbionts:temperature (31C) | 0.524 | 0.181 | 2.89 | 0.004 |
| PSTR:symbionts:pCO2-current | 0.362 | 0.818 | 0.44 | 0.659 |
| PAST:symbionts:pCO2-current | 0.673 | 0.473 | 1.42 | 0.154 |
| PSTR:symbionts:pCO2-EOC | -0.179 | 0.418 | -0.43 | 0.669 |
| PAST:symbionts:pCO2-EOC | -0.180 | 0.335 | -0.54 | 0.590 |
| PSTR:symbionts:pCO2-extreme | -0.482 | 0.401 | -1.20 | 0.229 |
| PAST:symbionts:pCO2-extreme | -0.890 | 0.341 | -2.61 | 0.009 |
| PSTR:symbionts:temperature (31C) | 0.189 | 0.350 | 0.54 | 0.589 |
| PAST:symbionts:temperature (31C) | -0.607 | 0.281 | -2.16 | 0.031 |
| Conditional R2 | 0.280 | |||
| Marginal R2 | 0.139 |
Session information
Session information from the last run date on 2022-02-03:
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] janitor_2.1.0 rcompanion_2.4.1 car_3.0-11 carData_3.0-4
## [5] png_0.1-7 MASS_7.3-54 performance_0.7.3 wesanderson_0.3.6
## [9] RColorBrewer_1.1-2 gridGraphics_0.5-1 corrplot_0.90 Hmisc_4.5-0
## [13] Formula_1.2-4 survival_3.2-12 magick_2.5.2 ggpubr_0.4.0
## [17] vroom_1.5.4 lmerTest_3.1-3 lme4_1.1-27.1 Matrix_1.3-4
## [21] kableExtra_1.3.4 finalfit_1.0.3 ggfortify_0.4.14 cowplot_1.1.1
## [25] Rmisc_1.5 shiny_1.7.1 vegan_2.5-7 lattice_0.20-44
## [29] permute_0.9-5 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
## [33] tibble_3.1.3 tidyverse_1.3.1 plotly_4.9.4.1 openxlsx_4.2.4
## [37] corrgram_1.14 tidyr_1.1.3 ggbiplot_0.55 scales_1.1.1
## [41] plyr_1.8.6 dplyr_1.0.7 ggplot2_3.3.5 broom_0.7.9
## [45] readr_2.0.1 knitr_1.33
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.2.1 systemfonts_1.0.2
## [4] lazyeval_0.2.2 splines_3.6.3 TH.data_1.0-10
## [7] digest_0.6.27 htmltools_0.5.2 fansi_0.5.0
## [10] magrittr_2.0.1 checkmate_2.0.0 cluster_2.1.2
## [13] tzdb_0.1.2 modelr_0.1.8 matrixStats_0.57.0
## [16] sandwich_3.0-1 svglite_2.0.0 jpeg_0.1-9
## [19] colorspace_2.0-2 ggrepel_0.9.1 rvest_1.0.1
## [22] haven_2.4.3 xfun_0.25 libcoin_1.0-8
## [25] crayon_1.4.1 jsonlite_1.7.2 Exact_2.1
## [28] zoo_1.8-9 glue_1.4.2 gtable_0.3.0
## [31] webshot_0.5.2 abind_1.4-5 mvtnorm_1.1-2
## [34] DBI_1.1.1 rstatix_0.7.0 Rcpp_1.0.7
## [37] viridisLite_0.4.0 xtable_1.8-4 htmlTable_2.2.1
## [40] proxy_0.4-26 foreign_0.8-75 bit_4.0.4
## [43] stats4_3.6.3 htmlwidgets_1.5.3 httr_1.4.2
## [46] modeltools_0.2-23 ellipsis_0.3.2 mice_3.13.0
## [49] farver_2.1.0 pkgconfig_2.0.3 multcompView_0.1-8
## [52] nnet_7.3-16 sass_0.4.0 dbplyr_2.1.1
## [55] utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.1
## [58] rlang_0.4.11 later_1.3.0 munsell_0.5.0
## [61] cellranger_1.1.0 tools_3.6.3 cli_3.0.1
## [64] generics_0.1.0 evaluate_0.14 fastmap_1.1.0
## [67] yaml_2.2.1 bit64_4.0.5 fs_1.5.0
## [70] zip_2.2.0 coin_1.4-1 rootSolve_1.8.2.2
## [73] nlme_3.1-151 mime_0.11 xml2_1.3.2
## [76] compiler_3.6.3 rstudioapi_0.13 curl_4.3.2
## [79] e1071_1.7-8 ggsignif_0.6.2 reprex_2.0.1
## [82] DescTools_0.99.42 bslib_0.3.1 stringi_1.7.3
## [85] highr_0.9 nloptr_1.2.2.2 vctrs_0.3.8
## [88] pillar_1.6.2 lifecycle_1.0.0 lmtest_0.9-38
## [91] jquerylib_0.1.4 data.table_1.14.0 insight_0.14.3
## [94] lmom_2.8 httpuv_1.6.2 R6_2.5.1
## [97] latticeExtra_0.6-29 promises_1.2.0.1 gridExtra_2.3
## [100] rio_0.5.27 gld_2.6.2 codetools_0.2-18
## [103] boot_1.3-28 assertthat_0.2.1 nortest_1.0-4
## [106] withr_2.4.2 multcomp_1.4-17 expm_0.999-6
## [109] mgcv_1.8-36 parallel_3.6.3 hms_1.1.0
## [112] rpart_4.1-15 class_7.3-19 minqa_1.2.4
## [115] snakecase_0.11.0 rmarkdown_2.10 numDeriv_2016.8-1.1
## [118] lubridate_1.7.10 base64enc_0.1-3